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© Research
Publication : Molecular biology and evolution

SMS: Smart Model Selection in PhyML

Scientific Fields
Diseases
Organisms
Applications
Technique

Published in Molecular biology and evolution - 01 Sep 2017

Lefort V, Longueville JE, Gascuel O

Link to Pubmed [PMID] – 28472384

Mol. Biol. Evol. 2017 Sep;34(9):2422-2424

Model selection using likelihood-based criteria (e.g., AIC) is one of the first steps in phylogenetic analysis. One must select both a substitution matrix and a model for rates across sites. A simple method is to test all combinations and select the best one. We describe heuristics to avoid these extensive calculations. Runtime is divided by ∼2 with results remaining nearly the same, and the method performs well compared with ProtTest and jModelTest2. Our software, “Smart Model Selection” (SMS), is implemented in the PhyML environment and available using two interfaces: command-line (to be integrated in pipelines) and a web server (http://www.atgc-montpellier.fr/phyml-sms/).

https://www.ncbi.nlm.nih.gov/pubmed/28472384